After a roller-coaster year for Brazil, the latest allegations risk destabilizing Temer just six months after he took office, as he seeks to rescue Latin America's biggest economy from crisis.
Supreme Court judges yesterday ruled that Brazil's third-most powerful official, Senate president Renan Calheiros, 61, must face trial for alleged embezzlement.
He denies the accusations that he used public funds to make maintenance payments to a woman with whom he had a child.
In a fresh development in the Petrobras affair on Thursday, a source close to construction firm Odebrecht told AFP that 77 of its current and former executives had signed a plea deal with investigators.
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They agreed to cooperate with prosecutors in return for lighter sentences, said the source, who asked not to be named.
The 77 include the firm's jailed boss Marcelo Odebrecht, who was reported earlier this year to have named Temer in testimony to investigators.
Temer is not being formally investigated himself, but the Petrobras scandal has already driven several of his ministers to resign.
Brazilian media said the plea deal could lead to 100 more suspects being dragged into the sprawling Petrobras probe, dubbed Operation Car Wash by investigators.
Marcelo Odebrecht was handed a 19-year jail sentence in 2015 for corruption and money-laundering. The new plea deal could lead to his term being reduced.
The separate embezzlement case caught up with Calheiros as a battle between prosecutors and politicians was raising tensions.
Prosecutors threatened to resign, saying the reform would undermine Operation Car Wash.
Temer had previously vowed to block any attempt by legislators to grant themselves a corruption amnesty.
In the case now going to trial, Calheiros has insisted he made the maintenance payments out of his own funds.
But the Supreme Court judges said there was sufficient evidence to put him in the dock.
Calheiros and Temer were the leaders of the impeachment case that drove their leftist rival Dilma Rousseff from office.